Review Update on Potentially Zoonotic Viruses of European Bats Claudia Kohl * , Andreas Nitsche and Andreas Kurth Robert Koch Institute, Centre for Biological Threats and Special Pathogens, 13353 Berlin, Germany; [email protected] (A.N.); [email protected] (A.K.) * Correspondence: [email protected]; Tel.: +49-30-187-542-144 Abstract: Bats have been increasingly gaining attention as potential reservoir hosts of some of the most virulent viruses known. Numerous review articles summarize bats as potential reservoir hosts of human-pathogenic zoonotic viruses. For European bats, just one review article is available that we published in 2014. The present review provides an update on the earlier article and summarizes the most important viruses found in European bats and their possible implications for Public Health. We identify the research gaps and recommend monitoring of these viruses. Keywords: bats; virome; metagenomics; Issyk-Kul virus; SARS-like CoV; zoonoses; Zwiesel bat banyangvirus; Mammalian orthoreovirus; Lloviu virus 1. European Bat Viruses Bat viruses have been gaining worldwide attention following the outbreaks of SARS- Coronavirus (CoV), SARS-CoV-2, Nipah virus, Hendra virus, and Ebola virus. Worldwide sequences of 12,476 bat-associated viruses are available at NCBI Genbank and DBatVir Citation: Kohl, C.; Nitsche, A.; Kurth, (accessed on 31 March 2021) [1,2]. The highest number of sequences is available from Asia A. Update on Potentially Zoonotic (5225), followed by Africa (2728), North America (1889), Europe (1353), South America Viruses of European Bats. Vaccines (1065), and Oceania (216). In comparison to Asia and Africa, the number of European bat 2021, 9, 690. https://doi.org/ viruses discovered seems low. As virus species richness is positively correlated with species 10.3390/vaccines9070690 richness and abundance, it is coherent that more viruses are discovered in the species-rich tropical regions [3,4]. Additionally, the prominent examples of zoonotic bat viruses have Academic Editors: Davide Lelli and been emerging in Asia and Africa; this is consequential since the highest number of bat Ana Moreno viruses was detected on these continents. European bat species are covered by species protection through the European Commission (http://ec.europa.eu/environment/nature/ Received: 21 May 2021 legislation/habitatsdirective, accessed on 22 June 2021) and through the Agreement on the Accepted: 21 June 2021 Conservation of Populations of European Bats (www.eurobats.org, accessed on 22 June Published: 23 June 2021 2021); therefore investigative research requires special permission by local government bodies. This might contribute to the lower number of viruses detected in Europe and North Publisher’s Note: MDPI stays neutral America. Nevertheless, the viral richness discovered in European bats is high. with regard to jurisdictional claims in The current SARS-CoV-2 pandemic is once more underlining the importance of viral published maps and institutional affil- discovery in bats. If we can come back to databases containing the sequences of the viral iations. diversity in the respective hosts, it becomes more feasible to determine which measures need to be taken. This review aims to provide an overview on viruses discovered in European bats. In addition, we identify the research gaps, as data on critical factors necessary for an assessment of the zoonotic risk are rarely reported. For most of the viruses, Copyright: © 2021 by the authors. data is unavailable on viral shedding of infectious virus, prevalence of the virus in the Licensee MDPI, Basel, Switzerland. host population, abundance of hosts and habitat overlap with humans, identification of This article is an open access article potential transmission routes, and data on shedding seasonality. We discuss the potential distributed under the terms and anthropozoonotic and zoonotic transmission between bats and humans and propose to conditions of the Creative Commons further investigate certain bat viruses. Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). Vaccines 2021, 9, 690. https://doi.org/10.3390/vaccines9070690 https://www.mdpi.com/journal/vaccines Vaccines 2021, 9, 690 2 of 41 1.1. Bat Virus Discovery in Europe The first sequence of a European bat virus in the database was reported in 1995, and the oldest collected European bat specimens were from 1968 [1,5]. The greatest attention was paid to Rhabdoviruses before the virus discovery studies have been diversifying from 2007 on. Figure1 shows the number of published virus sequences over time, related to the respective viral family and order. However, another criterion to determine virus discovery in Europe is the number of published viruses by year of specimen collection, as shown in Figure2 that summarizes the number of published viruses by year of specimen collection. Figure2 displays that the number of discovered viruses and, we assume, likewise the efforts in specimen collection had grown ten-fold in 2007. This increase in sample collection and virus discovery studies may be the result of the increasing recognition of bats as potential reservoir host of emerging viruses. Bats were confirmed as reservoir host of Hendra virus in 2000 [6], Nipah virus in 2001 [7], SARS-like CoV in 2005 [8], and Marburg virus in 2009 [9]. In addition, they were postulated as potential host of Ebola virus in 2005, MERS-CoV in 2012, and SARS-CoV-2 in 2020 which still has to be confirmed [10–12]. Figure3 illustrates how the discovery of bat viruses has been diversifying from 2003 on, while virus discovery focused on Rhabdoviruses in bats until 2002. From 2003 on we see an increased discovery of CoV in European bats. On the one hand, this might be due to the fact that CoV (among other viruses) can be detected in feces samples and are therefore more accessible to research than other specimens (compare Figure4). On the other hand, CoV are very abundant in bats and have a high tenacity, making them more likely to be detected compared to e.g., Paramyxoviruses. Moreover, the lack of data on negative tested bats raises difficulties to draw conclusions [13–17]. Another factor is the availability of bat species for examination. Bat species are very divergent in their roosting and migration behavior, making it difficult to collect specimens from some species and easy from others. In contrast to studies in other areas of the world, the European bats are strictly protected; thus bat sampling is more complicated and results in a potential underrepresentation of the number of bat viruses reported. An overview on viruses discovered by bat species in Europe is given in Table1. It seems that most viruses were found in Myotis spp., Pipistrellus spp., and Eptesicus spp. Here also, without data on bats that were sampled but tested negative, it is hard to draw conclusions. Figure 1. Number of published virus sequences over time, related to the respective viral family and order (DBatVir [1]). Vaccines 2021, 9, 690 3 of 41 Figure 2. Number of published virus sequences by year of specimen collection (DBatVir [1]). Figure 3. Published virus sequences by year of specimen collection, related to the respective viral family and order (DBatVir [1]). Another reason for the generally increased detection of viruses could be the great progress in virus discovery methods during the same time-frame. While in the early years of virus discovery researchers had to rely on time-consuming cell-culture methods for virus detection, the “molecular evolution” was a game changer. Not only PCR, primer design, and capillary sequencing were becoming cheaper and thus widely available, also massive parallel sequencing methods were gaining attention. It was in 1994 when Canard and Safarti first published the baseline for Illumina sequencing technology [18]. In 2005 Margulies et al. published the massive parallel sequencing method of 454 sequencing [19]. In 2013 already, Roche shut down the 454 sequencing branch, as Illumina became market leader. Since 2014 portable sequencing via Oxford nanopore is on the rise [20,21]. Metagenomics and viromics have become standard applications in the virological research communities, leading to Vaccines 2021, 9, 690 4 of 41 increased virus discovery results in European bats [15,22–33]. However, isolation of viruses is still the gold standard in virology for subsequent functional characterization and it will be very hard to replace this method. Figure 4. Specimen type used for virus detection related to the respective viral family and order (DBatVir [1]). 1.2. Viruses Detected in European Bats Until now, the database of bat viruses comprises 1353 entries for Europe (accessed on 31 March 2021) [1]. A summary of all entries (viruses vs. bat species) can be found in Table1 . Table2 provides references, host bat species, and detection methods for all viruses found in European bats. Figure5 displays the number of viruses by family recorded for European bats. The majority of viruses recorded in the database belongs to the families Rhabdoviridae and Coronaviridae. Since the first review on zoonotic viruses of European bats in 2014 [2] various novel viruses have been discovered. In the following section we focus on these viruses that in our opinion could possibly pose a zoonotic threat to humans. The full and up-to-date list of European bats can be accessed online at the Database of Bat-associated Viruses (DBatVir) [1]. Figure 5. Number of viruses by family recorded for European bats in log scale (DBatVir [1]). Vaccines 2021, 9, 690 5 of 41